Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria

BACKGROUND: In silico comparative genomics approaches have been efficiently used for functional prediction and reconstruction of metabolic and regulatory networks. Riboswitches are metabolite-sensing structures often found in bacterial mRNA leaders controlling gene expression on transcriptional or translational levels. An increasing number of riboswitches and other cis-regulatory RNAs have been recently classified into numerous RNA families in the Rfam database. High conservation of these RNA motifs provides a unique advantage for their genomic identification and comparative analysis. RESULTS: A comparative genomics approach implemented in the RegPredict tool was used for reconstruction and functional annotation of regulons controlled by RNAs from 43 Rfam families in diverse taxonomic groups of Bacteria. The inferred regulons include ~5200 cis-regulatory RNAs and more than 12000 target genes in 255 microbial genomes. All predicted RNA-regulated genes were classified into specific and overall functional categories. Analysis of taxonomic distribution of these categories allowed us to establish major functional preferences for each analyzed cis-regulatory RNA motif family. Overall, most RNA motif regulons showed predictable functional content in accordance with their experimentally established effector ligands. Our results suggest that some RNA motifs (including thiamin pyrophosphate and cobalamin riboswitches that control the cofactor metabolism) are widespread and likely originated from the last common ancestor of all bacteria. However, many more analyzed RNA motifs are restricted to a narrow taxonomic group of bacteria and likely represent more recent evolutionary innovations. CONCLUSIONS: The reconstructed regulatory networks for major known RNA motifs substantially expand the existing knowledge of transcriptional regulation in bacteria. The inferred regulons can be used for genetic experiments, functional annotations of genes, metabolic reconstruction and evolutionary analysis. The obtained genome-wide collection of reference RNA motif regulons is available in the RegPrecise database (http://regprecise.lbl.gov/)

The Use of Health Care Services and Psychotropic Medication in a Community Sample of 9-Year-Old Schoolchildren with ADHD

Contains fulltext : 52748.pdf (publisher's version ) (Closed access)OBJECTIVE: To examine the prevalence of the use of health care services and psychotropic medication within a community sample (N = 283) of 9-year-old school children and, more specifically, to evaluate the use of prescribed stimulants. METHODS: Data from the second follow-up phase of the "Study of Attention Deficit Maastricht" (SAM) were analysed. Assessments at age 9 included a structured psychiatric interview with parents, behaviour and family situation questionnaire, IQ estimate and global assessment scale. Use of health care services and medication was obtained by the DICA-R and from the Youth Health Care records. RESULTS: About 190 children of the selected sample had at least one child psychiatric diagnosis, 26 (14%) of them were clinically referred and 12 (6%) received stimulants. Of the children with ADHD (N = 45), 10/45 (22%) received stimulants. Conversely, 2 out of 12 children who were treated with stimulants did not meet full DSM-IV diagnostic criteria, but were subthreshold ADHD cases. The treatment status was highly dependent on being clinically referred. CONCLUSION: The major finding of our survey is a lack of referral to child mental health services, and associated underdiagnosis and undertreatment, particularly in children with ADHD. There is a critical need to translate and implement the diagnostic and treatment guidelines to clinical practice

Carbohydrate Availability Regulates Virulence Gene Expression in Streptococcus suis

Contains fulltext : 127539.pdf (publisher's version ) (Open Access)Streptococcus suis is a major bacterial pathogen of young pigs causing worldwide economic problems for the pig industry. S. suis is also an emerging pathogen of humans. Colonization of porcine oropharynx by S. suis is considered to be a high risk factor for invasive disease. In the oropharyngeal cavity, where glucose is rapidly absorbed but dietary alpha-glucans persist, there is a profound effect of carbohydrate availability on the expression of virulence genes. Nineteen predicted or confirmed S. suis virulence genes that promote adhesion to and invasion of epithelial cells were expressed at higher levels when S. suis was supplied with the alpha-glucan starch/pullulan compared to glucose as the single carbon source. Additionally the production of suilysin, a toxin that damages epithelial cells, was increased more than ten-fold when glucose levels were low and S. suis was growing on pullulan. Based on biochemical, bioinformatics and in vitro and in vivo gene expression studies, we developed a biological model that postulates the effect of carbon catabolite repression on expression of virulence genes in the mucosa, organs and blood. This research increases our understanding of S. suis virulence mechanisms and has important implications for the design of future control strategies including the development of anti-infective strategies by modulating animal feed composition

Immunotoxins for targeted cancer therapy

Immunotoxins are proteins that contain a toxin along with an antibody or growth factor that binds specifically to target cells. Nearly all protein toxins work by enzymatically inhibiting protein synthesis. For the immunotoxin to work, it must bind to and be internalized by the target cells, and the enzymatic fragment of the toxin must translocate to the cytosol. Once in the cytosol, 1 molecule is capable of killing a cell, making immunotoxins some of the most potent killing agents. Various plant and bacterial toxins have been genetically fused or chemically conjugated to ligands that bind to cancer cells. Among the most active clinically are those that bind to hematologic tumors. At present, only 1 agent, which contains human interleukin-2 and truncated diphtheria toxin, is approved for use in cutaneous T-cell lymphoma. Another, containing an anti-CD22 Fv and truncatedPseudomonas exotoxin, has induced complete remissions in a high proportion of cases of hairy-cell leukemia. Refinement of existing immunotoxins and development of new immunotoxins are underway to improve the treatment of cancer